The tissue samples for the microarray study consisted of 10 patient-matched normal renal cortex and ccRCC tissues, five from stage I and five from stage II ccRCC.
Previously, we performed a pilot study consisting of microarray analysis on three groups of patients: seven stage I without recurrence, seven platin-sensitive advanced stage and six platin-resistant advanced stage ovarian tumours [ 2].
The TGCT microarray study here consists of five undifferentiated embryonal carcinoma samples and 12 differentiated testicular cell samples, which include both tumors and healthy samples [ 17].
The 111 informative ovarian carcinomas in tissue microarray used in this study consist of 82 serous, 12 mucinous, 12 clear cell, and 5 endometrioid subtypes (Table 1).
The human cDNA microarray used in this study consisted of 349 fully sequenced and annotated cDNAs as described in the Supplemental Table 1.
The Bovine Innate Immune Microarray developed in this study consists of 1480 characterised genes identified by literature searches, 31 positive and negative control elements and 5376 cDNAs derived from subtracted and normalised libraries.
The microarrays utilized in this study consisted of commercial preprinted slides or slides printed in-house using widely accepted techniques, and thus are representative of a wide cross-section of the microarrays currently employed in genomic research.
Oligonucleotide microarrays used for this study consisted of 13,297 70-mer oligos (Pig Array-Ready Oligo Set v. 1.0 and Pig Oligo Extension Set v. 1.0, Qiagen, Inc., Valencia, CA) each spotted once on a single slide.
The S. pneumoniae microarrays used in this study consisted of 3482 70-mer oligonucleotide probes from the genomes of 3 pneumococcal strains (TIGR4, R6 and G54) as well as 10 amplicons and 500 oligonucleotides (70-mers) from Arabidopsis thaliana which served as negative controls.
DNA microarray data used in this study consisted of dual dye arrays for 11 prokaryotic organisms and yeast from the KEGG expression database [ 40] and the Stanford microarray database [ 34].
